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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | database, data or information resource | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-08-04 09:40:48 | 3 | ||||
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Allopathfinder Resource Report Resource Website |
Allopathfinder (RRID:SCR_002702) | AlloPathFinder | software application, software resource, source code | Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure. | allosteric communication, allostery, allosteric, pathway, protein, residue, prediction, myosin, computational model, protein model, structure-based protein classification, protein classification, myosin allosteric communication |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; Jane Coffin Childs Memorial Fund ; NIGMS U54 GM072970; NIGMS GM33289 |
PMID:17900617 | Free, Available for download, Freely available | nif-0000-23327 | SCR_002702 | Predicting allosteric communication in myosin via a conserved residue pathway | 2026-08-04 09:40:43 | 0 | |||||
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DE-Sim Resource Report Resource Website |
DE-Sim (RRID:SCR_018770) | simulation software, software application, software resource | Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. | Object oriented, discrete event simulation, data driven modeling, oriented discrete event simulation, computation model simulation |
is related to: NumPy is related to: SciPy is related to: Pandas is related to: SIMULA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NSF 1649014; NIGMS R35 GM119771; Icahn Institute for Data Science and Genomic Technology |
Free, Available for download, Freely available | SCR_018770 | Discrete Event Simulation, object oriented Discrete Event-Simulation tool | 2026-08-04 09:44:24 | 0 | ||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data processing software, software application, software resource, data analysis software | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-08-04 09:44:25 | 8 | ||||||
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Protein Cross-Linking Database Resource Report Resource Website 1+ mentions |
Protein Cross-Linking Database (RRID:SCR_021027) | ProXL, proxl, Protein XL | web service, software resource, data access protocol, database, data or information resource | Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination. | Protein cross-linking, mass spectrometry data, analysis, visualization, sharing, structural analysis, quality control, private collaboration, public data dissemination |
uses: Kojak has parent organization: University of Washington; Seattle; USA |
NIGMS P41 GM103533; University of Washington Proteomics Resource |
PMID:27302480 | Free, Available for download, Freely available | https://github.com/yeastrc/proxl-web-app | SCR_021027 | Protein XL Database | 2026-08-04 09:44:42 | 5 | |||||
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Kojak Resource Report Resource Website 1+ mentions |
Kojak (RRID:SCR_021028) | data processing software, software application, software resource, data analysis software | Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets. | Mass spectra, cross-linked peptides identification, protein complexes analysis, novel data analysis, existing data analysis |
is used by: Protein Cross-Linking Database has parent organization: University of Washington; Seattle; USA |
National Science Foundation MRI grant 0923536; NIGMS P50 GM076547; NIGMS P50 GM08722150; NCRR S10 RR027584; NIGMS P41 GM103533 |
PMID:25812159 | Free, Available for download, Freely available | SCR_021028 | 2026-08-04 09:44:42 | 3 | ||||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, software application, software resource, image analysis software | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-08-04 09:43:50 | 13 | ||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-08-04 09:43:59 | 39 | ||||||
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RSRef Resource Report Resource Website 1+ mentions |
RSRef (RRID:SCR_017211) | data processing software, software application, software resource | Software for fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy. | Fitting, atomic, model, density, map, x ray, crystallography, electron, microscopy | NIGMS R01 GM66875; NIGMS R01 GM78538 |
PMID:23376441 | Free, Available for download, Freely available | http://xtal.ohsu.edu/software/rsref/readme.txt | SCR_017211 | 2026-08-04 09:44:06 | 1 | ||||||||
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mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | data processing software, software application, software resource | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-08-04 09:44:29 | 38 | ||||||
|
ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | portal, project portal, data or information resource | Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research. | Molecular tool, human proteome, proteome, human, peptide, data |
is related to: ProteomicsDB is related to: ProteomeXchange |
German Federal Ministry of Education and Research ; Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; NHGRI RC2 HG005805; NIGMS R01 GM087221; NCRR S10 RR027584; NIGMS P50 GM076547; European Research Council ; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-08-04 09:44:22 | 21 | |||||||
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GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | portal, project portal, data or information resource | Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression. | Gly-glycobiology Gen-information, glycobiology, glycans molecular properties, glycans biophysical properties, glycans functional properties properties, glycans, genes, proteins, lipids, pathways and ontologies, data, mutation and expression data, carbohydrate and glycoconjugate related data, | NIGMS 1U01GM125267; NIGMS R24 GM146616 |
PMID:31616925 PMID:32324859 |
Free, Freely available | SCR_023438 | GlyGen Portal | 2026-08-04 09:45:16 | 11 | ||||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | database, portal, project portal, data or information resource | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-08-04 09:45:18 | 55 | |||||||
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ConnecTF Resource Report Resource Website 1+ mentions |
ConnecTF (RRID:SCR_022577) | data access protocol, software resource, web service | Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation. | integrate transcription factor gene interactions, validate regulatory networks, gene regulatory network validation | NIGMS RO1-GM121753; NSF PGRP IOS-1339362; NSF PGRP IOS-1840761; NIGMS F32GM116347 |
PMID:33631799 | Free, Available for download, Freely available | https://github.com/coruzzilab/connectf_server | SCR_022577 | 2026-08-04 09:45:03 | 3 | ||||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, software application, image processing software, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-08-04 09:45:09 | 0 | ||||||||
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APA-Scan Resource Report Resource Website |
APA-Scan (RRID:SCR_022974) | data processing software, data analysis software, software resource, software application, data visualization software | Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data. | annotated and potential alternative polyadenylation events, gene downstream 3'-UTR, RNA-seq and 3'-end-seq data, two different biological conditions, polyadenylation events | NSF FET2003749; NIGMS R01GM113952; NIDDK DK097771 |
PMID:36171568 | Free, Available for download, Freely available | SCR_022974 | 2026-08-04 09:45:09 | 0 | |||||||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | web application, software resource | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NHLBI U54HL127624; NCI U24CA224260; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-08-04 09:45:11 | 108 | |||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | NIGMS 5T32GM080177; NCI 1R33CA212697; Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/, https://github.com/AllonKleinLab/SPRING_dev | SCR_023578 | 2026-08-04 09:45:18 | 24 | |||||||
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Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | data access protocol, software resource, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-08-04 09:45:18 | 11 | |||||||
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MicrobeJ Resource Report Resource Website 1+ mentions |
MicrobeJ (RRID:SCR_023914) | data processing software, data analysis software, software resource, software application, image processing software | Software tool for high throughput bacterial cell detection and quantitative analysis. Used to analyze bacterial cells. Used to process images derived from variety of microscopy experiments with special emphasis on large image sets. Performs intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. | bacterial cell detection, analyze bacterial cells, bacteria quantitative analysis, process images, intensity and morphology measurements, | is a plug in for: ImageJ | NIGMS GM51986; NIGMS GM113172; Indiana University Office of the Vice President for Research ; NCATS UL1TR001108 |
PMID:27572972 | Free, Available for download, Freely available | SCR_023914 | 2026-08-04 09:45:21 | 6 |
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